At Auschwitz, Treblinka, Birkenau, Belzec, Chelmno and Sobibor the Nazis established the Sonderkommando, groups of Jewish male prisoners picked for their youth and relative good health whose job was to dispose of corpses from the gas chambers or crematoria. Some did the work to delay their own deaths; some thought they could protect friends and family, and some acted out of mere greed for extra food and money these men sometimes received. The men were forced into this position, with the only alternative being death in the gas chambers or being shot on the spot by an SS guard.

At Auschwitz, the Sonderkommandos had better physical conditions than other inmates; they had decent food, slept on straw mattresses and could wear normal clothing. Sonderkommandos were divided into several groups, each with a specialized function. Some greeted the new arrivals, telling them that they were going to shower prior to being sent to work. They were obliged to lie, telling the soon-to-be-murdered prisoners that after the delousing process they would be assigned to labor teams and reunited with their families. These were the only Sonderkommandos to have contact with the victims while they were still alive. The SS carried out the gassings, and the Sonderkommandos would enter the chambers afterward, remove the bodies, process them and transport them to the crematorium. Other teams processed the corpses after the gas chambers, extracting gold teeth, and removing clothes and valuables before taking them to the crematoria for final disposal. The remains were ground to dust and mixed with the ashes. When too much ash mounted, the Sonderkommandos, under the watchful eyes of the SS, would throw them into a nearby river.

At Treblinka about 200 men were in charge of removing the corpses from the gas chambers. At Auschwitz the Sonderkommando working in the crematoria initially numbered 400 men, but the number was raised during the mass murder of Hungarians in 1944 to about 1,000 men. At Auschwitz and Birkenau, the Sonderkommando were responsible for sorting the suitcases, packages and other items with which the prisoners arrived on the trains. These items were taken to a storage area of the camp euphemistically called "Canada," where the "Clearing Commando" would unpack them, sort them, and prepare them for dispatch to Germany.

Despite the better conditions in which the Sonderkommando lived at the camps, most were eventually gassed as they became increasingly weak or sick from camp conditions. The Nazis also did not want any evidence of their horrific acts to remain, and therefore decided to kill those prisoners who witnessed their actions.

In October 1944, the Sonderkommando team at Birkenau learned that the Germans intended to gas them. At the camps, an underground movement had been planning a general uprising for some time, but it never happened. The remaining Sonderkommandos decided to take their fate into their own hands, and, on October 7, the group in charge of the third crematorium at the camp, the Birkenau Three Sonderkommando, rebelled. They attacked the SS with makeshift weapons: stones, axes, hammers, other work tools and homemade grenades. They caught the SS guards by surprise, overpowered them and blew up a crematorium. At this stage they were joined by the Birkenau One Kommando, which also overpowered their guards and broke out of the compound. The revolt ended in failure. There was no mass uprising, and within a short time the Germans succeeded in capturing and killing almost all the escapees.

About 100 of approximately 2,000 Sonderkommando from Auschwitz survived. In 1980, a student doing excavation work near the crematory III at Birkenau discovered a thermos containing a note from one of those survivors. Marcel Nadjari was deported from Thessaloniki to Auschwitz in 1944. “We all suffer things here that the human mind cannot imagine,” Nadjari wrote in a text he secretly penned in late 1944, then stuck in a thermos, wrapped in a leather pouch and buried in the soil near Crematorium III before the camp was liberated in early 1945. “Underneath a garden, there are two endless basement rooms: one is meant for undressing, the other is a death chamber,” Nadjari wrote. “People enter naked and when it is filled with about 3,000 people, it is closed and they are gassed….After half an hour, we would open the doors, and our work began,” meaning transferring the corpses to the crematoria where “a human being ends up as about 640 grams of ashes."

The Sonderkommandos tend to be regarded very negatively by most survivors, and to a certain extent the Jewish establishment in general. In the camps, the Sonderkommandos were seen as unclean, and the writer Primo Levi described them as being “akin to collaborators.” He said that their testimonies should not be given much credence, since they had much to atone for and would naturally attempt to rehabilitate themselves at the expense of the truth. Those who were members of the Sonderkommando, however, state they had no choice in their job, and they were as much victims of Nazi oppression as other prisoners in the concentration camps.